International Journal of Genomics

International Journal of Genomics / 2004 / Article

Conference paper | Open Access

Volume 5 |Article ID 154820 |

Karen Eilbeck, Suzanna E. Lewis, "Sequence Ontology Annotation Guide", International Journal of Genomics, vol. 5, Article ID 154820, 6 pages, 2004.

Sequence Ontology Annotation Guide

Received17 Nov 2004
Revised24 Nov 2004
Accepted25 Nov 2004


This Sequence Ontology (SO) [13] aims to unify the way in which we describe sequence annotations, by providing a controlled vocabulary of terms and the relationships between them. Using SO terms to label the parts of sequence annotations greatly facilitates downstream analyses of their contents, as it ensures that annotations produced by different groups conform to a single standard. This greatly facilitates analyses of annotation contents and characteristics, e.g. comparisons of UTRs, alternative splicing, etc. Because SO also specifies the relationships between features, e.g. part_of, kind_of, annotations described with SO terms are also better substrates for validation and visualization software.This document provides a step-by-step guide to producing a SO compliant file describing a sequence annotation. We illustrate this by using an annotated gene as an example. First we show where the terms needed to describe the gene's features are located in SO and their relationships to one another. We then show line by line how to format the file to construct a SO compliant annotation of this gene.

Copyright © 2004 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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